User: raf4

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raf420
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r***@cumc.columbia.edu

Posts by raf4

<prev • 18 results • page 1 of 2 • next >
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Answer: A: discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db a
... Jim, Got it! I thought that downloading org.Mm.eg.db_3.4.0 fresh would be sufficient. I have not updated Bioconductor/R because I have a technical problem with my mac which forces me to reboot frequently. Once that is solved (probably by reinstalling the OS). I will update R/Bioconductor.   Th ...
written 9 hours ago by raf420
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Comment: C: discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db a
... Jim, Thank you, as always but I still am not getting all the genes (I am still on R 3.3.3 because there is an intermittent  problem with permissions on my mac which I want to solve before I update. Should that make a difference). > select(org.Mm.eg.db,keys="GO:0044339",column="SYMBOL",keytype= ...
written 1 day ago by raf420
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discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
... Dear Bioconductor, I find fewer genes for a given GO term in mouse with the org.Mm.eg.db than with teh online AMIGO server. I am wondering if the difference is due to delays in updating org.Mm.eg.db, or for some other reason. Here is my R session  library(AnnotationDbi) > library(org.Mm.eg.db) ...
gene ontology written 9 days ago by raf420
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, When the reads were aligned with the same algorithm, the glitch disappeared. Thanks and best wishes, Rich ...
written 4 months ago by raf420
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Comment: C: Problem running featurecounts in Rsubread on GFF file
... I believe I found part of the problem. I should  not have used the patched sequence. I am currently downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38 ...
written 4 months ago by raf420
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Comment: C: problem running featurecounts using hg38 in-built annotation
... I believe I found the problem. I should  not have used the patched sequence. I am currently downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38_no_alt_ ...
written 4 months ago by raf420
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problem running featurecounts using hg38 in-built annotation
... Dear List, I am having trouble running feature counts as implemented in Rsubread on my mac My script is: library(Rsubread) b1.res<-featureCounts(files="b1.res.bam",annot.inbuilt="hg38",isPairedEnd=TRUE,requireBothEndsMapped=FALSE) I get an output file with numbers instead of gene names and n ...
featurecounts hg38 written 4 months ago by raf420
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Comment: C: Problem running featurecounts in Rsubread on GFF file
... an addendum, It ran to completion with teh following output file" b1.res.bam NA    22698646 I will now try it with the internal annotation, but please let me know if the hg38 annotation can be applied to the patch. THANKS! Rich       ...
written 4 months ago by raf420
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Problem running featurecounts in Rsubread on GFF file
... Dear Bioconductor list: I have aligned some paired end reads to the human genome assembly CRCh38.p7 with R subread. I am now trying to count the reads with feature counts. It is taking over an hour on my mac, and as I recall it should run faster. This is teh first time that I have used featurecount ...
rsubread gff featurecounts grch38.p7 vs hg38 written 4 months ago by raf420
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Answer: A: Rsubread crash on Mac during alignment
... Dear Wei and Yang, I am sorry that I didn't get back to you. The person whom I was helping when I found the bug went elsewhere. I am curently using the new version and it works fine. Thanks and best wishes, Rich ...
written 4 months ago by raf420

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